{"id":"W4414640476","doi":"10.1101/2025.09.29.678898","title":"<i>De novo</i> design of phosphotyrosine peptide binders","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Chemical Synthesis and Analysis","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Division of Chemistry; National Institute of Allergy and Infectious Diseases; National Cancer Institute; Spark Therapeutics; Washington Research Foundation; Bill and Melinda Gates Foundation; National Science Foundation; Open Philanthropy Project; Defense Threat Reduction Agency; Defense Advanced Research Projects Agency; Cancer Research UK; Leona M. and Harry B. Helmsley Charitable Trust; Advanced Research Projects Agency; National Institutes of Health","keywords":"Phosphorylation; Epidermal growth factor receptor; Peptide; SH2 domain; Tyrosine phosphorylation; Protein–protein interaction; Plasma protein binding; Binding site; Protein design","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002676433,0.0004237429,0.0002514345,0.0001513193,0.000136061,0.0003562521,0.000608574,0.00038096,0.001156113],"category_scores_gemma":[0.0002470766,0.000223203,0.0003242448,0.00009973164,0.0002228747,0.0003049736,0.0005091507,0.0004802766,0.0004438279],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005379292,"about_ca_system_score_gemma":0.0002652338,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003766044,"about_ca_topic_score_gemma":0.0004302762,"domain_scores_codex":[0.9998764,0.00001732911,0.000006217577,0.00002661523,0.00004600963,0.0000274724],"domain_scores_gemma":[0.9999332,0.00001039978,0.00001666677,0.00001061507,0.00001583946,0.00001323801],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0001225408,0.0001192823,0.0009395675,0.000232573,0.00004767123,0.0001287719,0.00006759108,0.1868799,0.751937,0.01688827,0.001511732,0.04112506],"study_design_scores_gemma":[0.00003439903,0.0003118912,0.0003549959,0.00001057888,0.00001782243,0.0001390259,0.00001710354,0.6036189,0.3816113,0.002606963,0.01125303,0.00002413905],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.3223496,0.0009290892,0.6608322,0.0003308014,0.0000971844,0.0001219068,0.0002164903,0.001918517,0.01320431],"genre_scores_gemma":[0.812587,0.000403675,0.1828247,0.0001522441,0.00001396656,0.0001556611,0.0002169257,0.0002299131,0.003415942],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.001156113,"threshold_uncertainty_score":0.003902972,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0103421274111351,"score_gpt":0.2135642149392082,"score_spread":0.2032220875280731,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}